Land use change alters the hydrochemical features, nutrient outputs, and community structure of aquatic photosynthetic organisms in watersheds and has an important impact on C, N, and P biogeochemical processes. In shallow water environments, sediments are the most important burial sites for C, N, and P; however, the factors underlying the control of their deposition by land use changes remain unclear. In this study, the rela-tionship among hydrochemical features, aquatic photosynthetic organism community structure, and C, N, and P deposition in surface waters associated with different land uses was studied at the Shawan Karst Water-Carbon Cycle Test Site, Puding, SW China, by combining field monitoring and laboratory experiments performed over a complete hydrological year from September 2018 to August 2019. The results indicate that (1) OC and TN deposition showed small differences among ponds associated with five land uses, while TP was significantly higher in ponds associated with shrubland and grassland than in ponds of cultivated land, bare soil, and bare rock. (2) Cultivated land increased OC and TN deposition by increasing N and P output and planktonic algae biomass in surface waters, while grassland and shrubland ponds mainly by increasing DIC output and macro-phyte biomass. (3) Compared with cultivated land, grassland and shrubland significantly enhanced TP deposition by promoting the deposition of calcium-bound P and biogenic P from macrophytes and their epiphytic algae in surface waters. In conclusion, the shift of cultivated land and bare soil to grassland and shrubland may be conducive to the formation of benign aquatic ecosystems and stabilization of C, N, and P sinks in karst shallow surface waters.